Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.09 kDa 
• Atom Count: 1717 
• Residue Count: 192 
• Unique protein chains: 2

5DC4

CRYSTAL STRUCTURE OF MONOBODY AS25/ABL1 SH2 DOMAIN COMPLEX, CRYSTAL A

• DOI: 10.2210/pdb5DC4/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-23 Released: 2016-03-02 
• Deposition Author(s): Wojcik, J.B., Koide, A., Koide, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.190 
• R-Value Work: 0.144 
• R-Value Observed: 0.147 

Literature

Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface.

Wojcik, J., Lamontanara, A.J., Grabe, G., Koide, A., Akin, L., Gerig, B., Hantschel, O., Koide, S.

(2016) J Biol Chem 291: 8836-8847

• PubMed: 26912659 
• DOI: 10.1074/jbc.M115.707901
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Bcr-Abl is a constitutively active kinase that causes chronic myelogenous leukemia. We have shown that a tandem fusion of two designed binding proteins, termed monobodies, directed to the interaction interface between the Src homology 2 (SH2) and kinase domains and to the phosphotyrosine-binding site of the SH2 domain, respectively, inhibits the Bcr-Abl kinase activity. Because the latter monobody inhibits processive phosphorylation by Bcr-Abl and the SH2-kinase interface is occluded in the active kinase, it remained undetermined whether targeting the SH2-kinase interface alone was sufficient for Bcr-Abl inhibition. To address this question, we generated new, higher affinity monobodies with single nanomolar KD values targeting the kinase-binding surface of SH2. Structural and mutagenesis studies revealed the molecular underpinnings of the monobody-SH2 interactions. Importantly, the new monobodies inhibited Bcr-Abl kinase activity in vitro and in cells, and they potently induced cell death in chronic myelogenous leukemia cell lines. This work provides strong evidence for the SH2-kinase interface as a pharmacologically tractable site for allosteric inhibition of Bcr-Abl.

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Organizational Affiliation: 

From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tyrosine-protein kinase ABL1	A	123	Homo sapiens	Mutation(s): 0  Gene Names: ABL1, ABL, JTK7 EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens) Go to UniProtKB:  P00519
NIH Common Fund Data Resources
PHAROS  P00519 GTEx  ENSG00000097007

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
AS25 monobody	B	95	Homo sapiens	Mutation(s): 0  Gene Names: FN1, FN
Find proteins for P02751 (Homo sapiens) Go to UniProtKB:  P02751
NIH Common Fund Data Resources
PHAROS  P02751 GTEx  ENSG00000115414

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.190 
• R-Value Work: 0.144 
• R-Value Observed: 0.147 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.281	α = 90
b = 74.928	β = 90
c = 39.229	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-08-23 
• Released Date: 2016-03-02 
Deposition Author(s): Wojcik, J.B., Koide, A., Koide, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM090324
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM07281
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30CA014599

Revision History 

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Data collection
• Version 1.2: 2016-05-11
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence